Trial transcript: Day 12 (October 19), AM Session, Part 2

Q. Professor Behe, I'd like to turn our attention
now to Darwin's Black Box. What you explain in Darwin's Black Box
is that, modern science has been able to explore life at the
molecular level in a way that was not possible with Darwin, is
that right?

Q. And then you say, in the late 20th century, we
are in the flood tide of research on life, and the end is in
sight. The last remaining black box was the cell, which was
opened to reveal molecules, the bedrock of nature, the last black
box, correct?

Q. And the -- Matt, if you could pull up page 39,
please, and highlight the bottom paragraph there at the bottom.
This is the place in Darwin's Black Box where you explain what
you mean by irreducibly complex?

Q. Matt, could you pull up the tweaked definition
that he created? And I have inserted the words which is
necessarily composed to make this paragraph consistent with the
tweaking you described you did in response to Alan Orr. And I'm
going to read that. And I've called it here the modified
definition of irreducible complexity from Darwin's Black Box.

What it says is, By irreducibly complex, I mean a
single system which is necessarily composed of several
well-matched, interacting parts that contribute to the basic
function, wherein the removal of any one of the parts causes the
system to effectively cease functioning.

An irreducibly complex system cannot be produced
directly, that is by continuously improving the initial function
which continues to work the same mechanisms by slight successive
modifications of a pre-cursor system, because any pre-cursor to
an irreducibly complex system that is missing a part is, by
definition, non-functional.

An irreducibly complex biological system, if there
is such a thing, would be a powerful challenge to Darwinian
evolution. Since natural selection can only choose systems that
are already working, then if a biological system cannot be
produced gradually, it would have to arise as an integrated unit
in one fell swoop for natural selection to have anything to act
on.

So that's the last paragraph on page 39 adding the
words that you did in response to Dr. Orr?

Q. And when you say, it would have to arise as an
integrated unit in one fell swoop for natural selection to have
anything to act on, what you're saying is, whatever the proposed
pre-cursor was, would die because it doesn't have all of its
parts?

A. No, that's not correct. Die is not -- the
function of a system is not to live, it's to do something
particular. You say that the system did not work, it did not do
its function. For example, the bacterial flagellum would not work
without the necessary parts.

Q. And, therefore, there would be no successive
generation because that flagellum would not move on to the next
generation?

A. No, that's not right. A bacterium that is
missing a flagellum would certainly go on and continue to grow.
It can reproduce and so on. But the flagellum doesn't work. And
this is from my article, I believe, in Biology and Philosophy,
where I responded to Professor Orr.

And in that article, I specifically said that he
had a misconception that irreducible complexity meant that an
organism could not live without this, without the system that we
were talking about. And that's not what I meant by it.

Q. So the organism with half a flagellum or parts
of a flagellum could continue to live in that circumstance, it
just wouldn't have an operating flagellum?

Q. And then you write, However, commentary by
Robert Pennock and others has made me realize that there is a
weakness in that view of irreducible complexity. The current
definition puts the focus on removing a part from an already
functioning system.

And then continuing on after footnote 5, you say,
The difficult task facing Darwinian evolution, however, would not
be to remove parts from sophisticated pre-existing systems, it
would be to bring together components to make a new system in the
first place.

Thus, there is an asymmetry between my current
definition of irreducible complexity and the task facing natural
selection. I hope to repair this defect in future work. That's
what you wrote, correct?

A. That asymmetry is not really relevant to
biological circumstances. In the sentence that you skipped over
in that paragraph, I talk about what Professor Pennock discussed
in his book in making this point.

If I could just quote from that. He says, Thus,
seeking a counterexample to irreducible complexity entower a
battle. Pennock writes about a part in a sophisticated
chronometer whose origin is simply assumed which breaks to give a
system that he posits can nonetheless work in a simpler watch in
a less demanding environment.

So I viewed Professor Pennock's objection -- of
course, Professor Pennock is a philosopher, and that was an
interesting philosophical turn on my discussion, I thought, but
that is not -- that is not -- I did not consider that to be
relevant to biology.

A. No, the particular pathway that Professor
Pennock had in mind where one assumes that one has a very
sophisticated pre-existing system whose origin has been left
unexplained and has just postulated, which then goes on to
breakdown and give less sophisticated parts, that is the part
that I don't think is really relevant to biology.

Q. If you start with the system and then break it
down removing parts, that's not relevant to biology?

Q. Right. And you're not testing the natural --
the difficult task facing evolution, which starts from the
pre-cursors and moves forward to the system you're studying.
You're going backwards. Isn't that what irreducible complexity
proposes?

A. It does not propose that anything goes
backwards. It asks, how do we identify this problem for Darwinian
evolution? And if you can remove a part, and a system no longer
works, then the system needs those parts to work.

And so the problem, how you put that together by
numerous successive slight modifications, as Charles Darwin
thought one had to do, is, I think, illustrated by that.

Q. Now you've used the expression, produced
directly. I think that's in the definition. Matt, if you could
pull that back up. And if I understand what you mean by directly,
it means, for example, in the case of the flagellum, that it has
to be steps in which there's a rotary motor that continues to
become the rotary motor, that is the flagellum?

A. Yes. By direct, I mean that it essentially
worked, as the definition says, it works by the same mechanism,
has the same number of parts; essentially, it's the same
thing.

Q. Same thing. And then if you could turn to page
40 of Darwin's Black Box. Matt, if you could highlight the first
paragraph. You acknowledge another possibility?

Q. I'm not asking you to agree with it. I'm asking
you, is that what an evolutionary biologist proposes?

A. Again, let me make clear what we're talking
about here. Some evolutionary biologists certainly think that
exaptation is real and that it's important and so on. But simply
saying that this part over here was exapted from that part over
here does not give an explanation of how random mutation and
natural selection could have gotten it from one state to the
other.

Q. But it is certainly, exaptation -- for example,
a bird wing developing from some kind of feathered structure on a
dinosaur that didn't necessarily allow flight, that's what
evolutionary biologists propose, and they call it exaptation?

A. That's entirely possible, and that's consistent
with intelligent design, because intelligent design only focuses
on the mechanism of how such a thing would happen. So the
critical point for my argument is, how such things could develop
by random mutation and natural selection.

A. That's correct, only to say that intelligence
was involved somewhere in the process.

Q. Okay. Now you go on in this passage and say, As
the complexity of an interacting system increases, though, the
likelihood of such an indirect route drops precipitously, and as
the number of unexplained irreducibly complex biological systems
increases, our confidence that Darwinian's criterion of failure
has been met and skyrockets toward the maximum that science
allows?

What you're saying there is, you know, it could
happen, I'm not ruling it out, but it's really improbable?

A. Not explicitly, but as a biochemist who
understands what it takes to, for example, for a protein to
function, for two proteins to bind specifically to each other,
and so on, I rely on my experience of that in arriving at this
conclusion.

Q. Sorry. Couldn't resist. We've gone a long time.
But you agree that intelligent design, as opposed to just Michael
Behe, is making an argument for intelligent design far beyond the
cellular level, correct?

Q. And, for example, in Pandas, that's certainly
in play intelligent design of not just biochemical structures but
higher level forms?

A. Well, let me just correct myself. They're not
basing it on my argument in regard to irreducible complexity, but
they are basing it on the purposeful arrangement of parts, which
is certainly what I discuss in Darwin's Black Box.

Q. In Darwin's Black Box, you talk about a
purposeful arrangement of parts, and you actually say, you know,
using that standard, almost anything looks design, right?

A. Amazing in a different sense. Of course, when
you're talking about physical beauty, now you're thinking more of
an aesthetic and philosophical concept, yes.

Q. The features seem to be arranged in a way that
gives it great attractiveness?

A. Well, okay, but you're now speaking of
something that I was not speaking of. When I talked about the
purposeful arrangement of parts, it was for some function of the
system, not necessarily to be perceived as pretty.

Q. And they function in conjunction with each
other to do things, create gravity, light, things like that, that
are pretty remarkable?

A. Gravity is remarkable. Light is remarkable. But
you're going to have to be very careful about the sorts of
conclusions you draw from these things, because -- and simply
because you don't want to just become overenthused about the
beauty of nature and try to turn that into an argument.

Q. But it actually -- I mean, it functions. Light,
I mean, it functions. And gravity, it functions?

Q. And we don't rule out natural explanation for
all of these amazing phenomena, do we?

A. Well, you're going -- I don't rule out natural
explanations for anything, including intelligent design.
Intelligent design does not rule out natural explanations.
However, you're going to have to make some distinctions between
how phenomena work and what phenomena strike many people as
somehow ordered to, or is necessary for specific purposes such as
the existence of life.

Q. You just described it. I mean, you got to be
careful about how we're talking about how everything has
different functions when we're making assessments about whether
the natural explanations are valid?

Q. So he's not saying, the flagellum is a machine,
he's saying, it resembles a machine?

A. No, he's saying, it resembles a machine
designed by a human. There are other machines in the cell that
may not resemble machines designed by humans, but I think, as
many people can see when looking at an illustration of the
bacterial flagellum, this is a machine that looks like something
that a human might have designed.

Q. Okay. And when you quoted to -- and he's also
saying, you know, other cellular systems don't resemble machines
so much, right? More so than other motors, the flagellum
resembles a machine designed by a human?

A. He's saying that more other machines in the
cell don't so much resemble machines designed by humans, but he
is certainly not saying that they are not machines, at least in
my reading.

And in that issue -- not -- in a previous issue of
Cell, the one that I pointed to earlier, a number of scientists
were discussing molecular machines that do not resemble things
that do not visually resemble machines that we have in our
world.

Q. But here he is saying, resembles a machine
designed by a human. That's your point, right?

Q. Now the intelligent designer, when he was
forming a bacterial flagellum millions or billions of years ago,
you're not suggesting he was actually modeling his design after a
manmade rotary motor which didn't exist until the last
century?

Q. Yeah. You're talking about things that resemble
machines designed by humans. You're not suggesting that the
intelligent designer, when the -- when he or she or they designed
the first bacterial flagellum millions or billions of years ago,
was modeling its design after manmade rotary motors which didn't
exist until the last century?

A. I'm not quite sure how exactly to address this
question. When you're inferring design, you do not ask yourself
whether a designer had some particular, you know, look in mind.
You're asking whether, in the structure of this system, you see a
purposeful arrangement of parts.

And I think, in the case of the bacteria
flagellum, the fact that it does resemble something from our
everyday world is due to the fact that its function is similar to
some things that we find in our everyday world such as propulsive
motors, like outboard motors on boats, and, therefore, the
functional engineering requirements would be similar for such a
machine in the cell as well as in our everyday world.

Q. Another example you gave was, and just to be
clear, Dr. DeRosier is in no way suggesting that his article has
anything to do with intelligent design?

Q. Better yet. And what you quoted from him was,
Why do we call the large protein assembles that underlie cell
function protein machines? Precisely because, like machines
invented by humans, these protein assemblies contain highly
coordinated living parts. He used the expression, like a
machine?

Q. Now you don't understand it to say, he was made
like a mountain was, not by wind or erosion or physical processes
on land mass?

A. No, of course not. People use words like that
in loose senses all the time. But in this particular case, Dr.
Alberts was making a specific comparison to the physical
functioning of these things and liking it to the physical
functioning of machines in our everyday world.

They require a precise arrangement of parts. They
act by transducing energy in order to accomplish some function
and so on.

Q. So when the same announcer said, the running
back is like a bulldozer, that was closer?

Q. And that's true for the other articles you
cited about whether biochemical systems are machines as opposed
to being like machines?

A. Well, again, I think we're getting into a
semantical distinction -- or just into semantics. If something
acts like a machine, and something has a function, and so on,
then it is a machine.

Q. Now you talked at some length on Monday about
the issue of whether the type III secretory system might be a
pre-cursor to the bacterial flagellum, or the reverse, that it is
a descendent of the bacterial flagellum, or they might have been
a common ancestor, right? You looked at some articles on that
subject?

Q. They were just scientists trying to figure out
whether it was A that evolved into B, or B that evolved into A,
or A and B evolving from C?

A. That's right. They were taking the mechanism of
natural selection and random mutation for granted. They were not
demonstrating it. They were not making arguments for it. They
were taking it as an assumption.

Q. And in terms of what the order is, they have --
they haven't nailed it down yet, right?

A. Not only haven't they nailed it down, but they
have proposed completely opposite scenarios whereby one can't
tell which arose first or second or even if they arose from each
other at all.

Q. Okay. But scientists, as they do with many
subjects on which there's disagreement, may continue to be making
arguments and writing papers and submitting them to peer review
journals and doing experiments to see if they can come up with a
consensus answer on the subject?

A. Sure. And they may write books to try to come
up with an answer, too, as well.

Q. And this is -- this Exhibit 724 is an article
in the Minnesota Daily. It's an opinion piece. And it says,
Intelligent Design 101, Short on Science, Long on Snake Oil. And
it goes on to describe --

MR. MUISE: I'm objecting that his use of this
document again is hearsay. He doesn't have recollection of this,
of this conversation. I'm not sure if he's going to be using this
to try to refresh his recollection.

MR. ROTHSCHILD: It recounts a conversation, and I
am going to ask Professor Behe whether that conversation
occurred.

MR. MUISE: He's going to ask him the conversation,
Your Honor, he can't just read --

THE COURT: Well, to the extent that you're going
to try to characterize the -- I think you've appropriately
characterized what the exhibit is, Mr. Rothschild. So why don't
you move on to your question.

MR. ROTHSCHILD: Okay. He has expressed a vague
recollection of what happened, so I'm going to read him the
passages in here.

Q. Just for some more foundation. In the first
paragraph, it says, Intelligent design's leading scientist, Dr.
Behe, a professor of biochemistry, visited the U, which I
understand to be the University of Minnesota, last week as a
guest of the McLauren Institute, and that, in fact, did
occur?

A. Okay. This paragraph says, Much to Dr. Behe's
distress, the TTSS is a subset of the bacterial flagellum. That's
right, a part of the supposedly irreducible bacterial outboard
motor has a biological function.

Q. And I'm not going to ask you about whether you
were distressed or not. But the next paragraph then says that he
asked you about this at lunch, correct?

A. We had lunch, and I recall a conversation about
this, but again, I don't recall many details.

Q. Okay. And according to Dr. Kurzinger, you
acknowledged that the claim that --

MR. MUISE: Objection, Your Honor. He's referring
to an editorial, and he's trying to recount this as an exact
conversation. Dr. Behe doesn't have recollection of what
occurred. This article has no relevance.

THE COURT: The next paragraph starting with, when
I asked Dr. Behe, I think, is where you're going.

Q. It says, When I asked Dr. Behe about this at
lunch, he got a bit testy, but acknowledged that the claim is
correct. Paren, I have witnesses. He added that the bacterial
flagellum is still irreducibly complex in the sense that the
subset does not function as a flagellum.

My question here is, is Mr. -- Dr. Kurzinger's
account that you agreed that the claim that the TTSS is a subset
of the bacterial flagellum, did you agree to that?

A. I don't recall, but I would, if I was going to
answer it very carefully, I would make a lot of distinctions
before saying so.

Q. Okay. And then you go on to say that you still
think -- well, I'll leave that. Your argument is that, even if
the type III secretory system is a pre-cursor to the bacterial
flagellum, is a subset, the bacterial flagellum is still
irreducibly complex because that subset does not function as a
flagellum?

Q. Yeah. Under this scenario of slow design --
which was what I experienced with my kitchen -- at some period of
time, the bacterial flagellum wouldn't have had all its parts
until the design was completed?

Q. Natural selection also suggests that there was
a subset of parts that would eventually comprise the bacterial
flagellum, but didn't work as the bacterial flagellum?

A. No. Natural selection, if I remember your
question correctly, natural selection does not suggest that.
People see that there is a subset of proteins in the flagellum
which share a lot of sequencology with proteins that act as a
type III secretory system.

Nobody, nobody has said how natural selection
could get you the type III secretory system, the flagellum could
get you from the -- even if you had the type III secretory
system, nobody has said how you could get from that to the
flagellum. Nobody has said how you could get from the flagellum
to the type III secretory system.

So this is an example again of conflating
different levels of evolution. We see evidence for common
descent, evidence for relationship, but we see nothing, nothing
that bears on the question of random mutation and natural
selection.

Q. Let me see if I've got this right. In natural
selection, the argument is that, there was a subset of parts,
right, like the type III secretory system, that eventually
evolved to become the bacterial flagellum, right? That's the
argument?

Q. I'm not asking you to agree with the argument,
Professor Behe. I'm just trying to walk us through this. The
argument for the evolution of something like the bacterial
flagellum, just to use that as an example, is that, at sometime
it had a subset of proteins, maybe looking something like the
type III secretory system, and eventually it evolved to become
the bacterial flagellum? That's the argument, right?

A. I would have to see the argument written down.
As you characterize it, I'm not quite sure what it is.

Q. Okay. But you're not disputing that the theory
of evolution says, at some point we had a subset of proteins,
then we had eventually all the proteins that make up whatever
system we're discussing?

Q. Then we've got slow design, and there we have
no mechanism at all, no description of a mechanism?

A. We have no description of a mechanism. We do
infer design though from the purposeful arrangement of parts.

Q. Now yesterday, I asked you some questions about
the designer's abilities. And you said, all we know about its
abilities is that it was capable of making whatever we have
determined is design. That's the only statement we can make about
the designer's abilities?

Q. And the only thing we know scientifically about
the designer's motives or desires or needs is that, according to
your argument, the only thing we would know scientifically about
that is that it must have wanted to make what we have concluded
as design?

A. I might say that, it might be a very indirect
process by which such a thing was made. So when you say that the
designer made the flagellum, it is not necessary to think that
somehow the protein parts of this were somehow immediately
brought together. It might have been a long process.

Q. Did the intelligent designer design each and
every protein of the flagellum?

A. That is a difficult question to address, and
there's lots and lots of distinctions to make. When you ask
whether the parts of the flagellum themselves require design, you
have to then focus in on those parts.

As I tried to emphasize earlier in my testimony
when we talk about parts, some people have a simple view, picture
in their minds something simple, but each of the parts is itself
a very complicated molecular entity. And as my work with David
Snoke shows, that even getting small changes in pre-existing
proteins, that is parts, is no easy task. So the question --

A. So that's actually an excellent question. Did
those parts themselves also have to be designed? And I think
right now, the question is open.

Q. Did the intelligent designer identify -- design
every individual flagellum in every bacteria or just the first
lucky one?

A. Well, since organisms, biological organisms can
reproduce, of course, then if one has the genes and the proteins
and information for a flagellum, then by the normal processes of
biological reproduction, more copies of the -- of that structure
can occur.

Q. And did the designer also design every mutation
of the flagellum since its inception?

A. No, you can't -- you certainly can't say that.
There is certainly random processes that go on in our world, or
for processes, that for all we can tell, certainly appear to be
random. So there's no -- nothing that requires us to think that
any mutation, any change that subsequently occurs to this
structure either was intended or -- was intended.

A. Is it observable? Hum. We can certainly observe
mutations, but unless the mutations and changes and so on further
go on to form a purposeful arrangement of parts, then we cannot
deduce simply from their occurrence that they were designed.

Q. That scientific -- after teaching them about
intelligent design, sign -- and telling them that, that is a
scientific proposition, that right now, scientifically, we can't
even tell you that an intelligent designer exists? Is that what
you want taught to high school students?

A. Well, let's make a couple distinctions. First
of all, when I say, when you use the word taught, again, a lot of
people have in mind instructing students that this is
correct.

A. Well, I'm sorry. I was unable to figure out
exactly what you meant. If you're asking --

Q. Tell them about it, Professor Behe. Make them
aware. Give them information.

A. Make them aware that some people say that, from
the purposeful arrangement of parts, we can conclude that
something was designed, but many other questions we can't
determine, including whether there were multiple designers,
whether the designer is natural or not, whether the designer
still exist? Yes, I think that would be a terrific thing to point
out to students.

It shows the limitations of theories. It shows
that some evidence bears on one topic, but does not bear on
others. I think that would be terrific pedagogy.

Q. Right. Okay. You've taken the position in this
courtroom that intelligent design is open to direct experimental
rebuttal, correct?

Q. And the way you said this could be done, and
why don't we turn to that document, which is Exhibit 718. If you
could turn to page 697. Matt, if you could highlight in the
second paragraph the passage that starts, To falsify such a
claim, and go to the bottom of the paragraph.

And you're asking the question here, or stating,
intelligent design is open to direct experimental rebuttal,
correct?

Q. And you said, To falsify such a claim, a
scientist could go into the laboratory, place a bacterial species
lacking a flagellum under some selective pressure, for mobility,
say, grow it for 10,000 generations, and see if a flagellum, or
any equally complex system, was produced.

If that happened, my claims would be neatly
disproven. Now the test you've described, that would falsify the
claim, your claim that the bacterial flagellum is irreducibly
complex in the way you've described it, and could, in fact,
evolve from pre-cursors, right, if that was successful?

A. That would show that my claim that it required
design -- required intelligent design was incorrect.

Q. Let's break that down. You have this concept of
irreducible complexity, right?

Q. And this test would, if it was successful,
demonstrate that the bacterial flagellum is not irreducibly
complex. We can, in fact, put a bacterial species lacking a
flagellum under some selective pressure, and eventually it's
going to get that flagellum, right?

A. Well, just a distinction. It wouldn't
demonstrate that it wasn't irreducibly complex. It would
demonstrate though that random mutation and natural selection
could produce irreducibly complex systems.

Q. Fair enough. It could evolve, and that would
falsify your claim that an irreducibly complex system, like a
bacterial flagellum, could not evolve through random mutation and
natural selection?

A. It is irreducibly complex. The question is
whether an irreducibly complex system can be put together by
random mutation and natural selection.

Q. Okay. So my question is, how would you falsify
the claim that a biological system, like the bacterial flagellum,
which is clearly a purposeful arrangement of parts, is not
intelligently designed?

A. Well, since it's an inductive argument, since
the purposeful arrangement of parts is an inductive argument,
then in order to falsify an induction, you have to find an
exception to the inductive argument.

So if somebody said that, when you see this
purposeful arrangement of parts -- and again, the -- as I stress,
the argument is quantitative, when there is a certain degree of
complexity and so on. If it was shown that that did not always,
did not always bespeak design, then the induction would not be
reliable, and we would -- so -- and the argument would be, would
be defeated.

Q. Now you, in fact, have stated that intelligent
design can never be ruled out, correct?

A. Well, I'm not sure -- I don't think I
would agree with that. I think the experiments described by Barry
Hall were actually in an attempt to do exactly that. He wanted to
see if he could, in his laboratory, re-evolve a lac operon. His
first step in that process in the mid 1970's were the experiments
that I discussed here yesterday, knocking out the beta
galactosidase gene.

His intention was, from things he has
written later, was to see how that would evolve and then knock
out two steps at a time, and eventually see how he could get
really the whole functioning system. But he had such trouble with
just getting that one step to go, and since he could not knock
out anything else, and get it to re-evolve, he gave up.

And so I would count his efforts as a test
of that, and say that the test, you know, that it was, it did not
falsify intelligent design thinking.

Q. And I had actually made a blood pact with
my co-counsel not to ask you about the lac operon, but now I had
to violate it.

Q. Okay. So you can't claim that the
proposition that the bacterial flagellum was intelligently
designed is a well-tested proposition?

A. Yes, you can, I'm afraid. It's
well-tested from the inductive argument. We can, from our
inductive understanding of whenever we see something that has a
large number of parts, which interacts to fulfill some function,
when we see a purposeful arrangement of parts, we have always
found that to be design.

And so, an inductive argument relies on the
validity of the previous instances of what you're inducing. So I
would say that, that is tested.

Q. Professor Behe, you say right here, here
is the test, here is the test that science should do, grow the
bacterial flagellum in the laboratory. And that hasn't been done,
correct?

A. That has not been done. I was advising
people who are skeptical of the induction that, if they want to
essentially come up with persuasive evidence that, in fact, an
alternative process to an intelligent one could produce the
flagellum, then that's what they should do.

Q. So all those other scientists should do
that, but you're not going to?

A. Well, I think I'm persuaded by the
evidence that I cite in my book, that this is a good explanation
and that spending a lot of effort in trying to show how random
mutation and natural selection could produce complex systems,
like Barry Hall tried to do, is likely to result -- is not real
likely to be fruitful, as his results were not fruitful. So, no,
I don't do that in order to spend my time on other things.

A. No, certainly not a waste of time. It was
very interesting. He thought that he would learn things. And he
did learn things. But they weren't the things that he started out
to learn. He thought that he would be able to see the evolution
of a complex system. And he learned how difficult that was.

Q. In any event, you have not undertaken the
kind of test you describe here for any of the irreducibly complex
systems you have identified?

Q. And you talked about selective pressures
that the bacterial flagellum could be exposed to, but a
laboratory could never recreate all the selective pressures that
have existed in the environment for the last three and a half
billion years?

A. Well, that's certainly true. But a
scientist -- scientists nonetheless try to understand parts of
nature, even though nature is very much bigger than a laboratory.
And in many other instances, such as people investigating origin
of life and so on, they nonetheless try to understand what the
proper environment would be to study, and so they can kind of
focus their efforts on what would be the most promising type of
environment, and so make it more likely to discover something
that was there than just focusing on the whole world.

Q. But it's entirely possible that something
that couldn't be produced in the laboratory in two years, or a
hundred years, or even in the laboratory that was in operation
through all of human existence, could be produced over three and
a half billion years? You have to agree with that, Professor
Behe?

A. It's entirely possible, but we can only
know if that is the case if we have, if we have experiments to
back it up or calculations to back it up.

Q. But intelligent design, that's a who
cares, right? It could be -- the universe could be -- or the
Earth could be billions of years old or 10,000 years old, and it
doesn't matter to intelligent design?

A. Intelligent design is not a person, so it
doesn't have feelings like you are describing.

A. Intelligent design is a scientific theory
that focuses on a particular question. There are many scientific
theories that focus on particular questions that do not have
anything to do with other interesting questions. The scientific
theory of intelligent design focuses on discerning design, and
that's it.

Q. Okay. And no human laboratory can
duplicate all of the selective pressures that have existed in the
billions of years that bacteria have been around?

A. That's correct. So we can't rule out all
explanations. We have to investigate to see what are likely.

Q. Professor Behe, the tests you proposed
here regarding the bacterial flagellum is like asking Dr. Padian
to grow a bird wing in a laboratory, isn't it?

A. The test that is sufficient for a theory
is proportional to what the theory claims. I'm no physicist, but
in physics, there have been claims, many claims that required
enormous amounts of effort by the entire physical community to
build large structures, took many years to do so.

And nonetheless, they thought that this
effort was worth it, because they wanted to be sure of the
answer. In biology, the claim that random mutation and natural
selection can produce systems like the flagellum or other
molecular machines is a very large claim. And one can't simply
say that because it would be hard to test it, we will just assume
it's true.

So if somebody wants to be sure or somebody
wants to -- wants to -- wants to respond to a skeptic with
evidence that would convince somebody that was not already
convinced of the theory, then there is no escaping the fact that
you have to show that your theory can do what you claim for
it.

Q. And so to do that, what scientists
advocating for the theory of evolution, including natural
selection, have to do is create a laboratory that repeats human
life -- that contains all of human life in deep time?

Q. In order to validate this big claim that
the theory of evolution makes, what you're really saying is,
they've got to create a laboratory that includes all of
biological life and operates over deep time?

A. No, I didn't say that at all. I said, if
it can be demonstrated that random mutation and natural selection
can produce complex systems, then intelligent design would be
falsified. One doesn't have to, you know, re -- show that
something of the complexity of a flagellum would be made.

But if one saw that something somewhat less
complex might be made in a reasonable time, then one might be
able to extrapolate. You'd have to pay attention to the details
of the system. So it's not, you know -- you don't need a
worldwide laboratory and a billion years to test this. You can do
things like Barry Hall tried to do.

Q. That can't recreate the opportunities
that were there for biological organisms throughout time?

A. There are always opportunities for
biological organisms. Biological organisms compete with each
other. If one manages to compete more successfully, it will -- it
will out grow others. And so there is no reason we can't expect
something, like in Barry Hall's experiments, to show us some new
interesting structure.

And if that occurred, that would be a real
feather in the cap of people who think Darwinian theory is
correct.

Q. Let's move onto the blood clotting
cascade. Now you showed us some slides yesterday, or the day
before, that show that certain organisms maintain a blood
clotting function with less than all the parts that mammals have,
correct?

Q. Now you've got this whole cascade. You've
got a diagram in Pandas. You got a diagram in your book, Darwin's
Black Box. And you show it as a multi-protein system that
includes that -- I think you said, intrinsic part of the
pathway?

A. These are all the proteins that have been
determined to affect blood clotting, yes.

Q. Okay. So -- but your claim in court is
that, eh, let's ignore parts of it, some of those parts don't
matter, we're just looking at a subset, right?

A. I made proper distinctions about what is
required and about what we don't have sufficient information to
make claims about that, yes.

Q. But those other parts never suggested are
not part of the blood clotting cascade, right, the intrinsic
pathway?

A. Well, I'm afraid I did. I -- well, I
quoted a section of my book showing that I was confining my
argument to the proteins at the end of the pathway.

Q. Matt, could you go to page 143 in Pandas
so that we can have the picture of the system. I understand what
you're saying, Professor Behe. You did indeed, in Darwin's Black
Box, define the blood clotting system in a particular way, right,
meaning --

A. Well, there are many more proteins that
affect blood clotting. But when I was talking about the concept
of irreducible complexity, I wanted to make sure that we were
talking about ones whose function was as clear as possible, so I
limited it to that.

Q. And so I guess what you're saying is,
part of the system -- part of the blood clotting system that
works in all of our bodies is irreducibly complex, but as it gets
more complicated, it's not irreducibly complex?

A. No, I didn't say that. I said that the
portion of the blood clotting system that I was focusing on was
irreducibly complex. There might be components which affect blood
clotting which can or can't be removed and help or not help but
not break the system. But I was focusing my argument on
irreducible complexity on the proteins I cited in my
testimony.

Q. You define the system in whatever way is
convenient to the argument?

A. I define the system very carefully to
make sure that people understand what I'm talking about. I use
the standard figure of the blood clotting cascade from a
biochemistry textbook, because that's what is understood as the
protein system that affects blood clotting.

Q. Now let me just make sure I understand
the argument. What I think you said was, when I looked at -- the
subset of the blood clotting cascade included fibrinogen,
prothrombin, proaccelerin, and activated Stuart factor. Those are
the things you say in Darwin's Black Box constitute the
irreducibly complex system?

Q. Okay. And, Matt, could you highlight in
the middle of the first column where it starts, We may try many
smaller sets. You say here, We may try many smaller sets of
components to get started; fibrinogen, prothrombin, activate the
Stuart factor, and proaccelerin. And then you give some other
alternatives. But then you say, death is nearly always the
certain result, right?

Q. Those are the four you just agreed were
enough to make your irreducibly complex system?

A. Well, those are the four that I said
that, if you knock them out of the current system, the system
would not function.

Q. So here you're saying, just having those
four -- you're saying, that's the irreducibly complex system, and
the rest of it we can forget, and now we look at that irreducibly
complex system, and death would be the certain result?

Q. You said, what I am talking about is
these four factors here, right? I won't say them again because
I'll just butcher them. Stuart factor and its friends. You said
in your testimony on Monday, those four, those you need?

Q. And you say, The function of the blood
clotting system is to form a solid barrier at the right time and
place that is able to stop blood flow out of an injured vessel.
The components of the system beyond the fork in the pathway --
that's the part we don't know so much about?

Q. The factors that -- it says, The
components of the system beyond the fork in the pathway are
fibrinogen, prothrombin, Stuart factor, and proaccelerin. And
those are the factors that, in Pandas, you say, if that's all you
got, you're dead?

A. I -- I -- these are the factors which, if
you break them, will cause the clotting system to stop
working.

Q. That's the system, right? That's what it
says in Darwin's Black Box? Those four components, that's the
system?

Q. Page 86, Professor Behe. We know it's not
the total system. There's a whole lot that we don't know about,
right, and that the puffer fish can do without. But the system
you're talking about, the single system that's irreducibly
complex, that's those four components, correct?

A. No. Again, I said that we should focus
our attention on those, because a lot more is known about them,
and if you remove them, the system will certainly be broken.

Q. Right above what we just read, it says,
The blood clotting system fits the definition of irreducible
complexity?

A. That begins, Leaving aside the system
before the fork in the pathway?

Q. Yes. Leaving aside the system before the
fork in the pathway, where some details are less well-known, the
blood clotting system fits the definition of irreducible
complexity. So we're leaving aside that stuff before the
fork?

Q. We're leaving the stuff aside that we
know the puffer fish can do without. And you're saying, The blood
clotting system fits the definition of irreducible complexity.
That is, it is a single system composed of several interacting
parts that contribute to the basic function, and where the
removal of any one of the parts causing the system effectively to
cease functioning.

It talks more about the function. It says,
The components of the system beyond the fork in the pathway are
fibrinogen, prothrombin, Stuart factor, and proaccelerin. That's
your irreducibly complex system, isn't it, Professor Behe?

A. No, it's not. Again, I was confining my
discussion to the point after the fork in the pathway because, as
I said in the book, much more is known about that. But the fork
in the pathway is essentially two different ways to activate the
pathway.

And while you can do without one way to
activate the pathway, you can't do without both ways to activate
the pathway. Something has to activate it.

A. Well, again, like I said, some of the
stuff. The puffer fish itself has the extrinsic pathway, which is
one way to trigger the remaining steps. It's missing the
intrinsic pathway. But nonetheless, it still has one way to turn
the pathway on.

Q. I'll withdraw that question, Professor
Behe. It's surely not your contention that the mistake you
understand Dr. Doolittle to have made basically invalidates the
possibility that the blood clotting system could have
evolved?

A. No, of course not. The only point I was
making with that discussion was that he did not know how
Darwinian processes produced it. It was not an argument saying
that -- or it was not -- did not go to the point of whether or
not that could happen.

Q. Okay. And that was an article, whether
right or wrong, that was not in a peer reviewed scientific
journal?

Q. And by contrast, how many peer reviewed
articles are there explaining the blood clotting -- why the blood
clotting cascade cannot evolve because it is irreducibly complex
in the way you describe?

A. Well, I'm going to say that the articles
which elucidate the structure of the blood clotting pathway are
the ones which demonstrate that. I will agree that there
certainly are no arguments or directly to that point. But as I
tried to show in my book, Darwin's Black Box, that's an
implication that can easily be drawn from those studies.

Q. So these are all those other articles
based on the research of other scientists that you interpret
differently than those scientists do?

Q. Okay. And how many peer reviewed articles
are there in scientific journals discussing the intelligent
design of the blood clotting cascade?

A. Well, again, since we infer design by the
purposeful arrangement of parts, then the peer reviewed articles
in science journals that demonstrate that the blood clotting
system is indeed a purposeful arrangement of parts of great
complexity and sophistication, there are probably a large number
of those.

Q. Again, those are those articles by other
scientists based on experimental research, right?

A. They are certainly by other scientists,
not by myself, and they are certainly based on experiments.

Q. And none of those articles are arguing
that the blood clotting cascade are intelligently designed -- is
intelligently designed?

Q. And before we leave the blood clotting
system, can you just remind the Court the mechanism by which
intelligent design creates the blood clotting system?

A. Well, as I mentioned before, intelligent
design does not say, a mechanism, but what it does say is, one
important factor in the production of systems, and that is that,
at some point in the pathway, intelligence was involved.